Current PhD Students

Xiaotong Li - Gerstein lab & Pusztai lab (2014) | ORCID: 0000-0003-1644-6835
Xiaotong Li's picture

Xiaotong is interested in next-generation sequencing data analysis, with a major focus on breast cancer. Currently she is working on whole genome sequencing analysis on inflammatory breast cancer, and heterogeneity analysis.

Jun Zhao - Kluger lab & Flavell lab (2014) | ORCID: 0000-0002-6671-0000
Jun Zhao's picture

Jun’s research focuses on the analysis of high-throughput sequencing data, RNA-seq, CRISPR, CLIP-Seq, etc. The goal is to help understand the genetic mechanisms of immune-related biological processes.

Daniel Chawla - Kleinstein lab (2015) | ORCID: 0000-0001-7667-9337
Daniel Chawla's picture
Dingjue Ji - Zhao lab (2015) | ORCID: 0000-0001-6288-8891

Frank is working on spatio-temporal transcriptomic data of brain. He is interested in developing new methods to identify the expression pattern of specific genes related to brain development. The new approaches are expected to help to understand the mechanisms of brain diseases like ASD.

Kevin Lopez - Brandt lab (2015) | ORCID: 0000-0002-2901-5674
Kevin Lopez's picture

Kevin Lopez works on multi model learning using deep learning and convolutional neural networks. He is also working on expanding the capabilities of Yale Image Finder by applying deep learning methods to classify images from PubMed publications.

Quan Zhou - Kleinstein lab (2015) | ORCID: 0000-0001-9602-2092
Quan Zhou's picture

Julian works with high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) data, especially in the context of B cell-mediated autoimmune diseases. He is interested in developing novel methods for inferring B cell lineages that help shed light on their developmental pathways.

David Chang - Brandt lab & Zhao lab (2016) | ORCID: 0000-0002-2065-0778
David Chang's picture

David Chang is studying recent advances in deep learning and NLP to enable effective integration of multiple EHR data modalities to improve information extraction

Hussein Mohsen - Gerstein lab (2016) | ORCID: 0000-0002-6263-8865
Hussein Mohsen's picture

Hussein’s main research interests are machine learning and cancer genomics. He is working on projects that leverage genomics big data to explore variation patterns in cancer. In particular, he is interested in developing machine and deep learning methods that study the underlying interaction between somatic and germline genetic variations in pan-cancer tumor types.

Nir Neumark - Kaminski lab & Coifman lab (2016) | ORCID: 0000-0002-5560-6136
Jay Stanley - Krishnaswamy lab (2016) | ORCID: 0000-0002-9227-8928

Jay studies learned representations of biological data, in particular graph representations and their processing.

Jiawei Wang - Zhao lab (2016) | ORCID: 0000-0003-2627-4897

Jiawei’s research interest lies in imaging genetics and mental diseases. He is working on gene expression analysis to help discover the etiology of PTSD and graphical models to study brain functional and structural network. 

Zhaolong Yu - Zhao lab (2016) | ORCID: 0000-0001-9585-2465
Zhaolong Yu's picture

Zhaolong’s current research focus is patient outcomes prediction based on multi-omics data. He is particularly interested in developing machine learning algorithms to better predict cancer patient outcomes.

Evan Cudone - McDougal lab (2017) | ORCID: 0000-0002-1055-1645
Jeffrey Fisk - Townsend Lab (2017) | ORCID: 0000-0002-1940-393X
Jeffrey Fisk's picture

Nick (Jeffrey) Fisk works on constructing phylogenetic trees to answer questions about cancer development, evolution, and the selective pressure treatment induces on the system. He also works on developing and implementing methods to optimize general phylogenetic experimental design.

Jiahao Gao - Gerstein lab (2017) | ORCID: 0000-0002-6311-3526

Jiahao focuses on the analysis of high throughput sequencing data, with special interest in ChIP-seq and other functional genomics technologies. He is currently working on denoising the ChIP-seq binding sites in order to improve the de novo inference of transcription factor binding motifs.

Scott Gigante - Krishnaswamy lab (2017) | ORCID: 0000-0002-4544-2764
Scott Gigante's picture

Scott’s research is focused the development of methods in deep learning and graph signal processing to understand the structure of single-cell genomics data, especially single-cell RNA sequencing data. He is particularly interested in how to make the most of many high-resolution noisy measurements, and how manifold learning techniques can facilitate this understanding.

Pranav Kantroo - Wagner lab & Machta lab (2017)
Tianxiao Li - Gerstein lab (2017) | ORCID: 0000-0002-9147-7511

Tianxiao is interested in applying novel machine learning techniques to inference of gene regulatory networks and 3D genomics. He is now working on developing novel methods to associate 3D genomics structures with gene regulatory elements.

Wei Liu - Zhao lab (2017) | ORCID: 0000-0003-2558-1377
Wei Liu's picture

Wei’s research is mainly focused on understanding genetic architecture and mechanisms of complex diseases. She is now working in developing statistical methods investigating disease-associated genes using multi-omics data including genetics, epigenetics and transcriptomics data. Wei is also interested in population genetics and causal inference.

Rihao Qu - Kluger lab & Flavell lab (2017) | ORCID: 0000-0002-8258-8287

Rihao’s research interests include high-throughput sequencing analysis and immunogenomics. He is working on developing computational and statistical methods to process high-dimensional single cell sequencing data and help understand the genetic mechanisms underlying immune pathways.

Yixuan Ye - Zhao lab (2017) | ORCID: 0000-0002-2643-665X
Yixuan Ye's picture

Yixuan’s research focuses on the genetic risk prediction for chronic diseases and cancer. She is currently working on exploring the interaction between gene, lifestyle and diseases. She is also interested in developing new methods to improve genetic prediction accuracy and the interpretation of polygenic risk score. 

Geyu Zhou - Zhao lab (2017) | ORCID: 0000-0002-4049-0193

Geyu’s research interest is statistical genomics and genetics. He is experienced in gene expression data analysis. He is currently working on developing statistical methods to compute polygenic risk score.

Edel Aron - Kleinstein lab (2018) | ORCID: 0000-0002-8683-4772
Egbert Castro - Krishnaswamy lab (2018) | ORCID: 0000-0001-7883-5241
Guannan Gong - Krumholz lab (2018) | ORCID: 0000-0002-4972-6705
Alex Grigas - O'Hern lab (2018) | ORCID: 0000-0002-1588-2996
Jeff Mandell - Townsend lab (2018) | ORCID: 0000-0002-3839-2543
Kyra Thrush - Levine lab (2018) | ORCID: 0000-0002-3991-9597
Ana Berthel - (2019)
Jeremy Gygi - (2019) | ORCID: 0000-0001-8567-7472
Diana Leung - (2019) | ORCID: 0000-0002-5999-9547
Wes Lewis - (2019) | ORCID: 0000-0002-1192-8862
Yaroslav Markov - (2019) | ORCID: 0000-0001-8778-4909
Eric Ni - (2019) | ORCID: 0000-0002-4530-0707
Vimig Socrates - (2019) | ORCID: 0000-0001-7955-9875
Andrea Tamminga - (2019) | ORCID: 0000-0001-9049-0928
Aarthi Venkat - (2019) | ORCID: 0000-0003-0298-0172
Mamie Wang - (2019) | ORCID: 0000-0002-3453-7805
Junchen Yang - (2019) | ORCID: 0000-0003-0988-1564
Seyedeh Maryam Zekavat - Zhao lab (2019) | ORCID: 0000-0003-4026-8944
Maryam is a MD-PhD student interested in combining germline and somatic genomics with deep phenotyping to discover and understand the causal factors of disease.
Biqing Zhu - (2019) | ORCID: 0000-0002-7428-6297